RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EAwjMu/RM_2409702.SatMay272052522023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1685245971 Database = /dev/shm/rModeler.EAwjMu/GCF_023864345.2_iqSchSeri2.2 - Sequences = 1455 - Bases = 9082822131 - N50 = 1099911349 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1201266652-1287071271 | [ 1 ] 1115462034-1201266652 | [ 1 ] 1029657416-1115462034 | [ 1 ] 943852798-1029657416 | [ 1 ] 858048180-943852798 | [ ] 772243562-858048180 | [ 2 ] 686438944-772243562 | [ ] 600634326-686438944 | [ 2 ] 514829708-600634326 | [ 1 ] 429025090-514829708 | [ ] 343220472-429025090 | [ ] 257415854-343220472 | [ ] 171611236-257415854 | [ 3 ] 85806618-171611236 | [ ] 2000-85806618 |************************************************** [ 1443 ] Storage Throughput = excellent ( 1201.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012782 bp ( 40011782 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:16:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:43 (hh:mm:ss) Elapsed Time Round Time: 00:37:31 (hh:mm:ss) Elapsed Time : 793 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14036 repeats masked totaling 4532685 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004386 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10004386 bp After Masking: 4179555 bp Masked: 58.22 % -- Input Database Coverage: 10004386 bp out of 9082822131 bp ( 0.11 % ) Sampling Time: 00:04:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 6455 HSPs Collected Number of families returned by RECON: 1399 Round Time: 00:11:13 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:12:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43953 repeats masked totaling 14285282 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008316 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30007316 bp After Masking: 13261830 bp Masked: 55.80 % -- Input Database Coverage: 40012702 bp out of 9082822131 bp ( 0.44 % ) Sampling Time: 00:14:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:25 (hh:mm:ss) Elapsed Time, 49671 HSPs Collected Number of families returned by RECON: 4876 Round Time: 00:41:58 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:35:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 137190 repeats masked totaling 45000216 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009006 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90006006 bp After Masking: 37034133 bp Masked: 58.85 % -- Input Database Coverage: 130021708 bp out of 9082822131 bp ( 1.43 % ) Sampling Time: 00:42:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:03:49 (hh:mm:ss) Elapsed Time, 287776 HSPs Collected Number of families returned by RECON: 13549 Round Time: 02:56:53 (hh:mm:ss) Elapsed Time : 591 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:45:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 483694 repeats masked totaling 156807781 bp(s). - TE Masking time 00:11:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046094 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 270039094 bp After Masking: 91705662 bp Masked: 66.04 % -- Input Database Coverage: 400067802 bp out of 9082822131 bp ( 4.40 % ) Sampling Time: 02:11:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 11:25:37 (hh:mm:ss) Elapsed Time, 955233 HSPs Collected Number of families returned by RECON: 30945 Round Time: 14:31:25 (hh:mm:ss) Elapsed Time : 1761 families discovered. RepeatScout/RECON discovery complete: 3265 families found Classification Time: 02:43:21 (hh:mm:ss) Elapsed Time Program Time: 21:42:21 (hh:mm:ss) Elapsed Time